[EMBOSS] fasta single-line sequence format?

[Peter Cock]

How about?: nowrapfasta

Peter C
.

On Tue, Aug 27, 2013 at 2:44 PM, Peter Rice <ricepeterm at yahoo.co.uk> wrote:
> Suggestions please for a format name to describe fasta format with the
> sequence always on a single line
>
> (needed for output only - it will be valid as format 'fasta' for input).
>
> Peter Rice
> EMBOSS Team
>
>
> On 27/08/2013 11:03, Niels Larsen wrote:
>>
>> Yes, i meant both input and output. It would not be default, so
>> hopefully no programs should get a long-line surprise. The speed
>> advantage is a single read for the whole sequence and not having
>> to remove newlines. Indexing sub-sequences with locators
>> becomes straightforward, the newlines don't get in the way. Most
>> genome packages use it, i think, including mine. Thanks, yes i
>> thought it must be quite easy to do ..
>>
>> Niels
>>
>> On Tue, 2013-08-27 at 10:41 +0100, Peter Rice wrote:
>>>
>>> On 27/08/2013 09:40, Niels Larsen wrote:
>>>>
>>>> EMBOSS list,
>>>>
>>>> I could not find a fasta single-line sequence format, is it
>>>> missing? having the sequence as a single line does not
>>>> violate fasta format i think, and many programs use it
>>>> because of speed and indexing convenience.
>>>
>>>
>>> You mean as an output format I assume? (it would be no problem for
>>> input).
>>>
>>> Easy to implement, but needs a name so you can so specify
>>> -osformat fastasingle (for example)
>>>
>>> It can also be an issue for applications that fail to check for very
>>> long input lines.
>>>
>>> I don't see any real benefit for indexing - you only need to point to
>>> the start of the ID line for that. Maybe there are applications that map
>>> the sequence string and want to have no extra characters.
>>>
>>> regards,
>>>
>>> Peter Rice
>>> EMBOSS Team
>>>
>>
>
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